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Roles of trans and cis variation in yeast intraspecies evolution of gene expression.

Sung HM, Wang TY, Wang D, Huang YS, Wu JP, Tsai HK, Tzeng J, Huang CJ, Lee YC, Yang P, Hsu J, Chang T, Cho CY, Weng LC, Lee TC, Chang TH, Li WH, Shih MC.

Mol Biol Evol. 2009 Nov;26(11):2533-8. doi: 10.1093/molbev/msp171. Epub 2009 Jul 31.


Expression evolution in yeast genes of single-input modules is mainly due to changes in trans-acting factors.

Wang D, Sung HM, Wang TY, Huang CJ, Yang P, Chang T, Wang YC, Tseng DL, Wu JP, Lee TC, Shih MC, Li WH.

Genome Res. 2007 Aug;17(8):1161-9. Epub 2007 Jul 5.


Roles of cis- and trans-changes in the regulatory evolution of genes in the gluconeogenic pathway in yeast.

Chang YW, Robert Liu FG, Yu N, Sung HM, Yang P, Wang D, Huang CJ, Shih MC, Li WH.

Mol Biol Evol. 2008 Sep;25(9):1863-75. doi: 10.1093/molbev/msn138. Epub 2008 Jun 23.


Effects of cis and trans regulatory variations on the expression divergence of heat shock response genes between yeast strains.

Li CM, Tzeng JN, Sung HM.

Gene. 2012 Sep 10;506(1):93-7. doi: 10.1016/j.gene.2012.06.034. Epub 2012 Jul 1.


Natural selection on cis and trans regulation in yeasts.

Emerson JJ, Hsieh LC, Sung HM, Wang TY, Huang CJ, Lu HH, Lu MY, Wu SH, Li WH.

Genome Res. 2010 Jun;20(6):826-36. doi: 10.1101/gr.101576.109. Epub 2010 May 5.


Inheritance of gene expression level and selective constraints on trans- and cis-regulatory changes in yeast.

Schaefke B, Emerson JJ, Wang TY, Lu MY, Hsieh LC, Li WH.

Mol Biol Evol. 2013 Sep;30(9):2121-33. doi: 10.1093/molbev/mst114. Epub 2013 Jun 22.


Evidences for increased expression variation of duplicate genes in budding yeast: from cis- to trans-regulation effects.

Dong D, Yuan Z, Zhang Z.

Nucleic Acids Res. 2011 Feb;39(3):837-47. doi: 10.1093/nar/gkq874. Epub 2010 Oct 8.


A yeast hybrid provides insight into the evolution of gene expression regulation.

Tirosh I, Reikhav S, Levy AA, Barkai N.

Science. 2009 May 1;324(5927):659-62. doi: 10.1126/science.1169766.


Contrasting Frequencies and Effects of cis- and trans-Regulatory Mutations Affecting Gene Expression.

Metzger BP, Duveau F, Yuan DC, Tryban S, Yang B, Wittkopp PJ.

Mol Biol Evol. 2016 May;33(5):1131-46. doi: 10.1093/molbev/msw011. Epub 2016 Jan 18.


Histone modification pattern evolution after yeast gene duplication.

Zou Y, Su Z, Huang W, Gu X.

BMC Evol Biol. 2012 Jul 9;12:111. doi: 10.1186/1471-2148-12-111.


Correlated changes between regulatory cis elements and condition-specific expression in paralogous gene families.

Singh LN, Hannenhalli S.

Nucleic Acids Res. 2010 Jan;38(3):738-49. doi: 10.1093/nar/gkp989. Epub 2009 Nov 19.


Contrasting properties of gene-specific regulatory, coding, and copy number mutations in Saccharomyces cerevisiae: frequency, effects, and dominance.

Gruber JD, Vogel K, Kalay G, Wittkopp PJ.

PLoS Genet. 2012 Feb;8(2):e1002497. doi: 10.1371/journal.pgen.1002497. Epub 2012 Feb 9.


The evolution of gene expression QTL in Saccharomyces cerevisiae.

Ronald J, Akey JM.

PLoS One. 2007 Aug 1;2(7):e678.


Local regulatory variation in Saccharomyces cerevisiae.

Ronald J, Brem RB, Whittle J, Kruglyak L.

PLoS Genet. 2005 Aug;1(2):e25. Epub 2005 Aug 19.


Revisiting the contribution of cis-elements to expression divergence between duplicated genes: the role of chromatin structure.

Li J, Yuan Z, Zhang Z.

Mol Biol Evol. 2010 Jul;27(7):1461-6. doi: 10.1093/molbev/msq041. Epub 2010 Feb 5.


Uncovering genetic regulatory network divergence between duplicate genes using yeast eQTL landscape.

Zou Y, Su Z, Yang J, Zeng Y, Gu X.

J Exp Zool B Mol Dev Evol. 2009 Nov 15;312(7):722-33. doi: 10.1002/jez.b.21290.


Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.

Khan Z, Bloom JS, Amini S, Singh M, Perlman DH, Caudy AA, Kruglyak L.

Mol Syst Biol. 2012;8:602. doi: 10.1038/msb.2012.34.


Phosphorylation of yeast transcription factors correlates with the evolution of novel sequence and function.

Kaganovich M, Snyder M.

J Proteome Res. 2012 Jan 1;11(1):261-8. doi: 10.1021/pr201065k. Epub 2011 Dec 9.

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